With-bead SPRI method for pond library construction. SPRI magnetic beads are added to the sheared DNA sample. DNA is selectively bound to SPRI beads, which are immobilized when the sample plate is placed on a magnet, leaving other molecules in the liquid phase. The liquid phase is removed and discarded. The sample plate is then removed from the magnet and DNA is eluted from the beads. Library construction master mixes are then added to eluant/bead solution. The DNA and SPRI beads then pass through three cycles of reaction, binding to beads (in the presence of polyethylene glycol (PEG)/NaCl solution) and cleanup/washing. The cycles carry out end repair, A-base addition and adaptor ligation, respectively. A final elution is then followed by PCR amplification.